Let's cut right to the chase here. Will the new V2 firmware give a clean signal out of the HDMI output? Answer after the read more :)
In a word, No. We think.
OK, we were a bit disappointed as well as this feature would unlock the potential of the 5D without having to crunch the pictures through that H264 nastiness. It's especially relevant now as there seems to be more and more portable HDMI recorders being announced every day.
If you haven't come across the Magic Lantern firmware before, it was written shortly after the 5D came out and tried to address some of its problems like the AGC on the audio. Canon have since fixed this with their firmware updates as well as adding a range of frame rates, so risking your 5D to the original hack has become less attractive.
This hasn't stopped the development of the ML firmware though. Some of the new features look pretty cool such as false colour and the circle focusing views.
Let's just get the warning in here before we go any further. You install the Magic Lantern firmware completely at your own risk. If you brick your camera it will make an expensive paperweight. Please read Moira's page thoroughly.
The firmware is still in Alpha so if you really need to get it running on your 5D, we suggest you join this Google Group.